test: Spawn subprocess directly for git commits (#14153)

Running git commit via the script or environment run method is
unnecessary, so switch to using subprocess.check_call like all of the
other VCS helpers.

In particular, script.run has been crashing in macOS CI due to a TOCTOU
race with a git lock file. (The script runner keep tracks of files
additions/changes/deletions, but we don't use that here.)